With the first column being genes, the second being the condition, the third being the replicate number and the fourth being the relative gene expression. So I have about 15 000 genes tested, with three conditions (alpha, beta and low) and about between 11-13 replicates per condition (13 alpha, 11 beta and 11 low).
I want to change the format so along the top I have the 35 replicates along the top (i.e. the 13 alpha, 11 beta and 11 low), the genes down the side as they already are a FPKM value for each individual for each gene, something as follows
My knowledge of coding is v limited, so if someone could help me, either with a Perl script or a simple UNIX command line script, that would be really great.
Thanks!
Edit: I've added in a screen shot of the input (on the right) and what I want the output to look like. I did it in excel to make it a bit easier to see the columns, but I have them in text files too.
output example. all the rows should look like the first two - i just had to add in a few spaces so they lined up correctly. and i just randomly added in the values into the table, but in the ouput they need to correspond to the FPKM values on the input.
Welcome to forums, thank you for using code tags for Inputs you have shown us in your 1st post. Also for RudiC's script yes you could run it as a command line command as well as you could make a script.ksh OR .sh OR .awk with proper permissions and can run it too. Also as always on a Solaris/SunOS system, change awkto /usr/xpg4/bin/awk , /usr/xpg6/bin/awk , or nawk.
Thanks that's worked I think. Would it be possible to maybe make it so that it copies the results into a text file, because i can't seem to copy and paste the terminal output into a word file because it's so many lines long. Thanks!
awk '
NR > 1 {LN[$1]; HD[$3,$2]; MX[$1,$3,$2] = $4}
END { printf "%10s", ""; for (i in HD) printf "%10s", i; print "";
for (j in LN) {printf "%10s",j; for (i in HD) printf "%10s", MX[j,i]; print ""}
}
' SUBSEP=, file > Output_file
This Output_file can be up to you and you could put it's name as your wish.
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12-03-2015
